Evangelion 1: Today is (not) Lost
by The Bluefire Phoenix
Summary: The year is 2016 and young Shinji Ikari is about to embark on a journey he never imagined. The secretive United Nations organization know as NERV has called him to Hong Kong. There he will have to face the greatest threat humanity has ever encountered. Can he survive the onslaught? Is the day truly lost?
1. Chapter 1

The following is a non-profit, fan work based off the respective works of Hideaki Anno and Guillermo del Toro

All rights belong to the original creators, Legend Pictures, LLC; and Gainax Company, Limited

The Bluefire Phoenix presents...

A _Project: Apocrypha_ Story...

_Evangelion 1: Today is (not) Lost_

Chapter I: First Contact

_"I can't say when or where the next strike will come from, but my research has concluded that Antarctica was just the beginning."_

_-Dr. Gendo Ikari, Private meeting with the UN Security Council, 7 January 2003_

6 April 2016  
Watch Station Bravo  
Just outside Honolulu, Hawaii

A thick haze of cigarette smoke hung over the small main chamber of the watch station. The blonde operator named Benny blankly stared at the screen. His orange Hawaiian shirt looked like it had seen better days.

Benny pulled out a fresh pack of cigarettes and began to pop one out of the cardboard container. Something appeared on his monitor. He looked up to see the blip.

His eyes widened. He quickly began typing into his computer terminal. Data began popping up all over the screen.

A band of sweat began to form on his brow. Benny felt his heart heave as a pattern began to form in his mind.

He finally drew a conclusion. Benny jumped up from his seat and ran to a red, wired phone on the other side of the room.

He picked up the receiver. A call dialed out. There was the click. "Director Ikari, this is Watch Station Bravo. Code word: Hell's Gate! Location: the Pacific!" Benny shouted.

Across the ocean in an underground bunker below Hong Kong, Gendo Ikari coolly gripped his own phone. "Understood," he replied. He hung the phone up and it disappeared into a hidden compartment on top of his desk.

Gendo sighed. His off grey uniform rippled a bit as he leaned forward. He finally buzzed for someone on his intercom.

"Marshal Pentecost here," the man on the other side said. His voice was strong but weary. Gendo smirked.

"Stacker, it's Gendo. What's Rei's status?"

"She won't be fit for duty for another week, why?" Stacker asked.

"The gates are open old friend," Gendo stated. Stacker remained silent for a brief moment.

"What are we going to do?" He finally asked.

"Activate our agent in Japan and recover the Third Child. We still have time before a Nephilim comes through. Worst case scenario the UN can buy us some more time for us to get a pilot. Move us to yellow alert," Gendo ordered. He could hear Pentecost swallow.

"Yes sir."

Comfort seemed to come easy for the sprawled out Misato Katsuragi. The woman was barely dressed and her snores reverberated around her bedroom.

The smell of alcohol clung to her breath. Freshly emptied beer cans littered the floor around her futon. A stuffed penguin doll was sitting near her head.

Her cellphone began to vibrate and ring. Misato stirred from her slumber. She used her arm to sweep for the disturbance.

"Hello," she spoke.

"Major Katsuragi, this is the Marshal. We need you to recover the Third Child," Pentecost gruffly said. Misato immediately sat up.

"But sir—Marshal I—I don't know who the Third Child even is!" She complained.

"I have sent you the necessary information and passes to print out. We have taken the liberty of informing his school about his sudden departure. Get him and get to Hong Kong. ASAP," the Marshal commanded.

"Yes sir," Misato said. She tried to perform a salute. Her had missed her forehead and poked her eye.  
"Ow."

A disappointed sigh entered Misato's ear. "And for the love of god, sober up a little first," the Marshal added.

Stacker hung up his phone. He brought his hands to his temples and started to rub them.

His office was small and Spartan save for a small number of pictures on his wall, the hallmarks of a military man. Even his black uniform was a reflection of his simple lifestyle. The only decor was a few ribbons and his eagle insignia that marked him as Pilot Marshal.

He finally stood and walked out of his office, towards the lift bank. Several security personnel straightened up as he past. Stacker held himself in such a way that he towered over the tallest of the guards.

The lifts were all busy at the moment, all except one. It had a security scanner instead of the traditional up and down buttons. He removed his ID card from around his neck and slid the magnetic strip down the receptor on the right side of the scanner.

English print started to appear. Pentecost, Stacker Position: Marshal, it read. Please Place hand on the Scanner for Finger Print Identification.

Stacker did as instructed. There was a brief flash.

A new message appeared: Access Granted.

The elevator doors parted. Stacker entered. The doors closed. No floor buttons could be found inside. Just the emergency buttons. The car began to slowly rise.

An ominous air gripped the ride. Stacker felt fine though. He knew this elevator better than any other person at the facility.

It only took a painfully long minute for the car to stop. The doors parted to reveal a large chamber. It was onyx black, covered in a sheen of white light from the large window behind a large desk. Engraved on the ceiling was the Sephirot.

Stacker cocked an eyebrow. "That's new," he muttered. Gendo was looking out the window.

"Indeed. I use it to remind me that all is revealed to those willing to search for it," Gendo said. He swiveled around. "You don't usually come to see me here, Stacker."

"I have ordered the extraction of the Third Child," the Marshal said. Gendo raised an eyebrow.

"A simple call would have been fine. Why make a personal report?" Gendo inquired.

"Are you sure about this?" Stacker retorted point-blank.

He could see Gendo fidget. "We can't risk being without a pilot. Once the UN realizes they are useless, they will need us to clean up the mess. Right now I just need someone to sit in the cockpit. Everything else should work out."

"You are taking an awfully big risk, Ikari. Outside the fact that if you are planning what I think you are, the selection of the Third Child will raise questions about your judgment as NERV's Director," Stacker said.

"I don't think the world will care too much about who saves it and their relationship to me," Gendo dryly remarked.

Stacker stepped ever closer to his friend. "I agree. It's our other patrons that concern me. This might not go over well with them," he lamented. He placed his hands on Gendo's desk and leaned forward.

"I'll handle them, Stacker. You just prepare our battle strategy," Gendo said. His intercom buzzed. "This is the Director."

"Command and Control here. We have movement in the breech. DNA pattern blue. It's a Nephilim."

Gendo sat there for but a moment. "Understood. We are now at red alert. Bring Unit-01 out Bakelite containment. Start tracking the Nephilim," he said. He returned his attention to Stacker.

"Is that wise? We haven't tested Unit-01," Stacker commented. He withdrew his hands and crossed his arms.

"Trust me, Stacker."

"That, old friend," Stack brought himself up to his full height, "is how I landed this job."

"I know what I'm doing."

"I believe similar words were spoken not fifteen years ago."

Gendo turned around to stare out the window. "We made a mistake then. Now we are forced to send children to cleanse our sins. It isn't particularly optimal, but we have no choice."

Misato wasn't having a great evening. It started when she couldn't find her dress uniform. She instead had to use her duty uniform which consisted of a tight fitting black dress with a white collar under her red combat jacket with black boots. Then she couldn't find her rank insignia for a whole twenty minutes. The only thing she didn't have to scramble for was her cross pendant.

It was a small comfort now that she was lost for the third time already looking for her target's private school. Her attention was caught by a large sign near an imposing gate. She read the sign and released a sigh.

The school was an elite campus, built in a western style. Rain started to fall just as Misato past the gates. The woman groaned as her windshield wipers failed to do more than spread the water around a little.

She pulled her little sports car up to the administration building. A figure was waiting at the front door. His face was obscured by an umbrella. Misato parked right by the figure.

She fiddled to free her cellphone from her back pocket as the boy loaded his suitcase in the boot and joined her. The woman looked at her charge just as she retrieved her phone. "Hey I, oh sorry. It's my boss," Misato greeted as her phone went off.

"Yes Marshal."

"Yes Marshal, I have the Third Child right here."

"What?"

"Yes sir. We're on our way."

Misato hung up the phone. She slumped in her seat. "That is downright unfair," she growled. Her hand started to shake.

"I'm sorry miss?" Her companion said. His voice was barely audible.

The woman smacked her forehead. "Sorry, I'm Major Misato Katsuragi, but Misato is fine," she said as she retracted her hand. The woman eyed the boy. He had soft, almost girl like features. His collared shirt was rumpled in places but his black pants seemed fine.

"And you must be Shinji Ikari."

"Yes ma'am," Shinji quietly answered.

_This is the kid they want to back up Rei? I hope the marshal know what he has coming._ Misato thought as she put her car in gear. She drove out of the school and quickly made pace for the airport.

Shinji blankly stared out the rain covered window. He let out a sigh.

"You must be nervous, huh?" Misato asked. Shinji disinterestedly shrugged.

"I guess so," he mumbled. The boy seemed to close himself off further.

_Oh my god, we just put fate of the world into this kids hands._ Misato dreaded to herself. "How long has it been since you've seen him?" She asked.

"Eight years I think. Why do you care?" Shinji asked. It sounded more curious than antagonistic.

It still felt as if he forced an icy dagger through her heart. "Sorry, I—I just wanted to have a conversation. If you don't want to talk, there is a file by your feet that you need to read," Misato dejectedly said. Shinji looked over at the woman. An all too easy frown fell across his face.

"Oh, no it's me who should apologize. Nobody at school wanted to talk to me. There was a rumor that my father is head of some secret organization. I guess they must have been scared or something."

"And what did your instructors tell you?"

"That he is important to the survival of humanity."

Gendo Ikari sat in a massive chamber with a virtual representation of the capital of the Philippians, Manila popping out of the entirety of his desk. He watched the city succumb to a massive humanoid form.

It stood on two webbed feet. The creature had a long reptilian tail that lashed out at nearby buildings like lightning. Two clawed hands swatted down helicopters and threw tanks across the city. Its head was massive and looked like a crab removed of its limbs. The creature's huge bony jaws outside of its head smashed open tanks. Slick tendrils grew from the back of head that reached down to its waste. At the center of its chest was a huge red orb.

Fighter jets zoomed through the air. Ground forces retreated and gunship laid down covering fire.

To his left was Stacker. The military man watched the battle with weary eyes. None of the human forces could land a blow. Their ammunition was halted in midair just a few meters out of reach. The explosions seemed to bounce off an invisible barrier.

Below the terrace where the head officers watched was Command and Control. Dozens of technicians scurried about as officers watched screens or reports flash by. In front of all of them was a massive television screen.

It kept switching between various feeds. But a HUD system on the perimeter gave general updates.

An officer stood up. Fear gripped his eyes. "Director, the Secretary General just cleared US forces to deploy an N2 Missile!" He shouted. Gendo merely adjusted his glasses as the last human forces disappeared from the map.

A single rod appeared near the top of the hologram. It rammed right into the creature. The hologram started to glitch and scramble. The television feeds turned to static.

Stacker took in a breath. Gendo just raised hand before any words escaped the other man. The images finally stabilized. Manila now had a giant smoking crater in the middle. Inside the hole, the creature stood unaffected.

A ringing red phone rose out of Gendo's desk. He picked it up. "Yes, Mr. Secretary General?" he said. "Yes sir. Give us two hours." Gendo put down the phone.

"Two hours is not a lot of time," Stacker commented. He crossed his arms.

"Maybe for the average military commander. That's why you're here. Start the Siren Song and prepare the city for ground assault. Whatever we do, we cannot let that thing get back into the water," Gendo commanded. He stood up and walked to the exit.

"You are in command here, Marshal," he said as he past Stacker.

"Aye sir. What are you going to do?"

"To make sure Unit-01 is ready for combat," Gendo said. The lift door opened and the man disappeared.

Stacker walked to the intercom station and opened up a facility wide channel. "Listen up, this is Marshal Pentecost," he said. All around headquarters, men and women paused to listen. "NERV has gotten the green light…."

"We all hoped this day would never come. But it has. It seems like this is the worse situation to start in. That doesn't matter. Right now I want you to think only of your job, alright? All hands to battle stations. Raise the Primary Containment Walls. This is not a drill."

The city of Hong Kong began to shift. Dozens of skyscrapers began to retract underground, leaving only smaller buildings behind. Massive, one hundred meters high panels began to rise out of the ground around the city limits.

A few dozen kilometers away, Shinji looked out the window of a small private plane. _Why would dad want me to work for him? What does NERV even do?_ He thought to himself. The files Misato had given him were clutched in his hands.

He looked over at his escort. Her hands were restlessly tapping against her arm. "Is something wrong?" Shinji asked.

Misato looked over at him. Shinji could see the terror in her eyes. "What's wrong? Nothing's wrong! Why would you say something's wrong?" Misato chattered.

"Are you afraid of flying?" Shinji inquired.

"I," Misato started. Shinji didn't look amused. "I have issues with planes. Let's leave it at that, okay?"

"Okay," Shinji responded. He started to rummage through his file once again. He barely got into the papers when the PA crackled to life.

"Attention passengers, please fasten your seat belts. We will be landing shortly," the pilot said. The plane began to descend onto a runway near a group of isolated building.

Misato gripped her seat hard enough that veins popped out of her hand. Shinji thought he heard her whisper something as the cabin bounced on touchdown. But he couldn't turn away from the city of Hong Kong.

Murky clouds hung overhead. But the city was bright and glistening in the primordial night.

The sense of wonder dissipated with a massive yank on his shirt collar right as the plane stopped. His papers nearly fell out of his hands. Misato dragged him towards the exit and down the steps onto the Tarmac.

A blonde haired woman was waiting for them. She wore a white lab coat over a blue blouse and white skirt. Her arms were locked across her chest. Misato nonchalantly rubbed the back of her head.

"He—hey Ritsuko, what's up?" Misato asked.

Ritsuko just glared. "You're late, Major," she looked to Shinji, "is this the Third Child?"

"Yeah it's him," Misato answered. Ritsuko reached out her hand.

"Dr. Ritsuko Akagi, head of NERV's R-and-D," she introduced herself. Shinji tentatively reached out to shake it.

"Um—I am—I am Shinji Ikari. Could you tell me why I'm—uh—here?" He asked. He weakly took the woman's hand.

A massive deafening roar followed by a flying ball of fire arcing across the sky from the south gave everyone pause. Ritsuko gave a half smile. "In short Mr. Ikari, that is why you are here," she said. She pointed southward.

_I don't like the sound of that._ Shinji thought. He reluctantly turned around to where she was pointing. A true hell-spawn rampaged through the buildings. The boy started to tremble. A reassuring hand gripped his shoulder.

"It will be okay," Misato reassured. "But now we need to get going."

Ritsuko nodded and walked towards the hanger. Misato and a worried Shinji followed her into the hanger. She led them to a tucked away corner. An air train was waiting. The trio entered the transport.

The train dropped down a floor then started to advance. It dipped deeper and deeper into a massive artificial chamber beneath the city. It was filled with trees and a lake fed by synthetic sunlight.

On the far side of the valley was a pyramid partially built into a lake. At the center was a huge station with various mag-train rails coming out of it on the ground. Most of rails ran to small launchers that aimed towards the ceiling. Other rails went to other facilities throughout the complex. Several other air train routs connected with the central station. A dozen or so elevators that led to the surface were scattered around the area.

"Welcome to the GeoFront kids. Humanity's greatest fortress," Ritsuko announced. Shinji couldn't tear himself away from the sights of the place. Misato was able to maintain an air of professionalism.

"This place is amazing!" Shinji declared.

"Sorry I can't give you the full tour yet. But right now we have to stay at the Cage," Ritsuko said as the train parked in the central facility. They departed the craft. Ritsuko led the other two away from the train station. She opened a highly secure door.

It parted to reveal a dark room. Just as Shinji slipped in the door rushed closed, leaving them in total darkness. He felt the floor move forward. It stopped with a hydraulic hiss followed by a lock.

"Shinji Ikari," Ritsuko said, "do you want to know why you are really here?"

Floodlights suddenly burst on. Shinji was staring straight at a purple, horned monster. Its void black eyes peered into the essence of Shinji. "Wha—what is this?" He stammered out. He began to flip through the pages of his files.

"I am afraid you won't find this listed in there," a man said from an observation deck above the machine. The cold voice made the hair on the back of his neck stand up and sent his heart beat into overdrive. Shinji looked up at the deck.

"Father," he whispered. The boy lowered his head back down.

Gendo glared down on his son. "Dr. Akagi if you'd cut to the chase," he said. The facility started to shake. "Before this place comes crashing down please."

Ritsuko nodded. "This, Shinji, is humanity's greatest weapon, code named Evangelion," she said. She locked eyes with Shinji. "And you will pilot it into battle."

The boy felt his heart trying to burst from his chest. He started backpedaling. Misato prevented him from walking off the edge into the chasm below.

"You—you're kidding right?" Shinji sputtered out. He looked up at his father. "I can't. I mean I don't even know how."

"You will receive instruction," Gendo coldly assured.

Shinji began to quiver. Only Misato's grip kept him from falling over. "Director, you can't just demand something like this of a kid!" The Major shouted.

The chamber shook again. "We don't have time to debate this Major. He either will or will not pilot. So what say you Shinji?" Gendo asked.

His son dropped to his knees. "Why? Why me?" He quietly asked.

"Because at the moment, we don't have anyone else," Gendo calmly admitted.

"Come on Shinji. We need you, the world needs. I promise you that I'll be here rooting for you!" Misato whispered. The boy looked up at the woman. All she could do was give him a reassuring smile just as the ground shook once more.

"What will it be, Shinji?" Gendo growled. Shinji stared at the purple creature. Something struck him like a jolt of electricity. He couldn't place the feeling it awoke.

The facility shook again. Bits of rock fell from the ceiling. "I'll—I'll do it," Shinji finally said. He hung his head. _Oh man, what have I gotten into? _He moaned to himself.

Ritsuko let out a sigh of relief. "Get Unit-01's Entry Plug prepped then move it to the dispatch tracks," she ordered.

The place came alive with mechanics. A huge tube lowered from the ceiling and a platform extended to it. Ritsuko led Shinji up to the tube. Misato slipped away to Command and Control.

Shinji was given two hair clips then helped into a seat in the tube. The tube sealed shut. A strange orange liquid filled the tiny chamber. "Gah! What is this stuff?" He shouted.

"It's called LCL, it will oxygenate your blood directly," Ritsuko said via the mech's communicator.

The doctor turned to one of her technicians. He brought up a window on his monitor. "The Third Child is ready for neural handshake."

"Listen up Shinji, what happens next is critical. I need you to clear your mind, okay?" She requested.

"Alright I'll try," the boy answered.

"Initialize handshake!" Ritsuko ordered. The technician pushed a button.

Shinji felt his body go numb. It felt like he was flying. Memories started to flash before his eyes. His body began to quiver.

Alarms rang out over the Cage. "He's rejecting the handshake! We need to cut the link!" the technician screamed.

"No, he can do this," Ritsuko said. He has to do this. She mentally amended.

Everything Shinji had buried deep inside now surrounded him. The loneliness, the pain, the doubt all swirled in his mind. It moved over his mind, applying needles over every bit of it.

Something warm and calming suddenly wrapped around his shoulders. His heart rate slowed and the world came into focus. He felt like he was safe.

"Link established! He's in the Drift, Synch Ratio at thirty percent and rising!" The technician enthusiastically shouted. Ritsuko smirked.

"Alright, Shinji I'm transferring you over to the Marshal. Good luck." Shinji heard an ominous click.

Command and Control was a mess. Operators were shouting stats and conditions. Stacker watched the hologram of the city. The monster was ripping it to pieces. His personal comm went off. It was a feed from Unit-01 with the Second Child as its pilot. Misato Katsuragi appeared out of the corner of his eye.

He hooked it up to his headset and picked up the line. "Shinji, I'm Marshal Pentecost. I'll be your commanding officer during your tenure at NERV. How are you?" He asked.

"Uh, not sure," Shinji answered. A green light appeared on Gendo's control pad.

"It will be alright, kid. Just listen to my orders and everything will be fine," Pentecost said. He pointed at Misato, getting her attention then gave her a thumbs-up.

Misato nodded. She walked to the railing. "What's our launch status?" She shouted down to the staff.

"Unit-01 is now at lift three and ready to go!" Someone shouted.

"Launch EVA!" Misato shouted. The room grew quiet. All eyes eagerly drifted up to the main screen.

_To Be Continued..._

* * *

A/N: Hello and thank you for reading my first foray into this site. I appreciate all constructive criticism and comments that you have. I plan to us this space in future chapters as a sort of blog. I'll answer FAQs, comment on what's going on in the story, and talk about fan fiction in general.

Okay, formalities over with? Alright, so the goal of _Project: Apocrypha _is to create something in the vein of the _Rebuild_ Movies using elements of _Pacific Rim _and a few of my own ideas.

So first chapter. Pretty standard EVA fair save for a few changes to bring it in line with _Pacific Rim_. Except the Nephilim, that's new. Yes it is my observant friends. I felt that Nephilim allowed me to capture the bestial forms of the Kaiju and the Lovecraftian nature of the Angels. Plus it ties into the project name well. Do not mistake that for lazy symbolism.

Expect plenty of perspective shifts in the chapters. It may make the story a bit harder to follow. But I think it flows with _Pacific Rim_'s theme of "we are all in this together." I also tried to make them as organically integrated as possible while making them blatantly obvious. If this is a problem for a lot of you, I'll improve it for you as we go along. However I really didn't want to litter each chapter with a million time stamps.

I read comics and watch Linkara, so continuity is very important to me. But if I use too many time stamps, I'd go insane trying to keep track of my own story. And no, "Meanwhile" and "Later" cuts will not work for me. Whenever I read those transitions, I always feel like I'm being taken out of the story just a little. That's just me.

Be on the look out for a couple of Easter Eggs in this chapter. They should be relatively easy to spot, but I _was_ the one who put them there.

Until next time, this is The Bluefire Phoenix signing off.


	2. Chapter 2

The following is a non-profit, fan work based off the respective works of Hideaki Anno and Guillermo del Toro

All rights belong to the original creators, Legend Pictures, LLC; and Gainax Company, Limited

The Bluefire Phoenix presents...

A Chapter of _Evangelion 1: Today is (not) Lost…_

Chapter II: The Power Within

_"The EVA's computer tried to reassert control and prevent the pilot from gaining system access. I believe this tripped the Control Rods and—well you saw what happened."_

_-From Dr. Ritsuko Akagi's Official Testimony for the "616 Report"_

Shinji heard Misato's command right after his stomach churned as his mech raced up the launch track. It stopped quicker than it began with a massive thud. He could now see the city around him.

His heart started to race when his eyes landed on the monster. "Shinji, relax. Just focus on walking. Imagine you are taking a step. Just make sure to avoid pulling out your power cord. If that goes then you'll have five minutes before you run out of battery power," Ritsuko said over his comm.

The boy closed his eyes. He imagined lifting his right leg and putting it down in front of him. The machine jerked a bit, but clumsily put its leg forward.

Command and Control watched the main monitor. There was a collective exhale as Shinji started to advance. Gendo arrived and took his seat. Pentecost joined him while Ritsuko walked over to Misato by the railing. The blonde woman pulled out a tablet computer.

"What do you think his odds are?" Misato whispered.

"Better than you keeping your job," Ritsuko dryly retorted.

"Really? We're going to do this now?"

"No, but considering he's hit a forty percent synch ratio, I would say we have a fighting chance."

Misato took a step back. "That's—that's incredible!" She sputtered.

Gendo looked pleased as he watched his son march towards the monster. He locked his fingers and placed them over his chin.

"You're doing fine Shinji. Now see that crystal in its chest? That is its weak spot. Get in close and destroy it," Pentecost said to his pilot.

Misato perked up. She walked right over to Gendo's desk and slammed her hands down, disrupting some of the virtual buildings. "You can't be serious. He lacks any skill to fight hand to hand!" She shouted.

"You are out of line, Major Katsuragi," Pentecost coolly said. The young woman growled.

"It's alright Misato. I can do it," Shinji responded. He was within a hundred meters of the creature, only fifty meters away from where he surfaced.

_Man, it was hard enough to get over here. How am I going to fight it?_ He thought. The creature finally noticed Shinji. It let a roar and charged him. "Oh, crap."

The creature put its full weight behind a body slam. Shinji was able to use his arms to buffer the blow. He kept his footing but failed to notice the creature's tail sneak in. It jabbed into the mech's shoulder right where it meet the arm.

Shinji let out a horrific scream of pain. The LCL started to bubble up. He used his other arm to grasp the creature throat. It dislodged its tail.

It used its claws to scratch at the mech's head. Shinji felt his skin split open from near the top of his right temple down to the edge of his lips. "Ghaaa!" He screamed as blood oozed from the wound.

Seizing the moment, the creature wrapped its head around Shinji and bit into his wounded shoulder. The boy tried to rip off the beast. But its bony jaws were clamped tightly on the mech. It began to tear off the arm. The claws on its hands continued to rip at the mech's back and accidentally pulled out the power cord.

In Command and Control, things started to go straight to hell. A large, red, digital clock started counting down. The crew all but went into panic mode.

"Get out of there Shinji!" Misato shouted into her headset. She slammed her fist onto the command table. The Marshal glared at her.

"I am still in command here major. One more outburst and I'll have you removed from here by force," Stacker stated.

"Director Ikari, you can't just let your son die out there!" Misato pleaded. Gendo just continued to watch the battle.

The monster finally ripped off Unit-01's arm and threw it across town and followed up by shoving the mech down. Shinji felt the flesh between his arm and shoulder tear apart on the inside. He cried out in anguish just as the clock hit zero across the board.

He felt the LCL run cold followed by the familiar dying hum of failing machinery. The chamber turned black. He could hear its thunderous footsteps close in on him.

Fear and despair gripped Shinji's heart. _So this how it ends?_ He thought. He felt the machine lifted into the air.

Something in the back of the boy's mind started to tingle. It felt familiar yet foreign. The feeling grew and grew until it swallowed him whole.

Ritsuko couldn't believe what she saw on her monitor. "Eject him now!" She shouted to the command staff. Misato gave a look to Stacker. He shook his head.

"Nothing's responding, doctor!" Someone shouted.

"Make it respond dammit! His synch ratio's off. He's vulnerable to contamination!" Ritsuko shouted back.

The director calmly watched the hologram. Unit-01 was lifting its arm, grabbing hold of the attacking creature's neck. A siren blared out. Misato ran over to the railing. "What's happening?" She asked. Ritsuko started to tremble.

"His Synch Ratio's jumped over one hundred percent! Control Rods are offline! It's—it's gone berserk," she whispered.

Misato felt her heart sink into her stomach. She looked up at the monitor to see Unit-01 regrow its lost limb.

"Unit-01 has deployed its AT-Field!" An operator called out.

A shimmering distortion formed around the mech's armored fist, using the regenerated arm to hold up the monster. It shattered an invisible wall around the spherical heart.

Unit-01 drove its fist right into the red object. It shattered on impact.

A massive flash of white and green took over the screen. The facility rumbled.

Over the city rose a giant cross that formed at the epicenter of a massive shockwave. Debris scattered dust all over the place.

Command and Control lost its signal. They struggled to return the feed. When they got it back, they were greeted by a wall of swirling dust. A shadow could be seen emerging from the cloud.

"My god," Misato whispered.

Sunrise revealed the damage done. Rubble lined the streets. A few wild fires roared. The massive corpse of the Nephilim dominated what was once the downtown area.

NERV crews were hard at work. They wore grey hazmat suits to keep the eerie blue gore off of their bodies. The stench of death and decay clung to the air. Trucks were loaded with the material and shipped off to an undisclosed location.

Ritsuko lazily fanned herself in the air conditioned command vehicle. She watched the dozen monitors showing the cleanup work. Her eyes moved from screen to screen, occasionally picking up the radio to issue orders.

The command vehicle was fairly spacious. It could comfortably seat four operators on the monitors as well as two commanding officers. A coffee maker bubbled with a soothing hum.

Misato stood off near the back door with her arms folded across her chest. Her fingers nervously drummed against her elbows. Strands of black hair started to fall out of place. Weird creases formed in her uniform.

Her eyes were glued to the monitor showing a crew working on Unit-01. The men and women were currently trying to get the Entry Plug to eject. They were tiny ants climbing upon a behemoth taller than a building.

"You should start worrying about yourself, Misato," Ritsuko dryly suggested. She took a sip from her coffee. Misato slammed her foot against the metal wall behind her.

"What the hell do I have to worry about? Shinji could be hurt or worse out there," Misato fired back.

Her blonde friend shook her head. She pulled off her glasses and looked up at the ceiling. "Do you remember that injured cat you found back in college?" Ritsuko asked.

Misato nodded, her eyes narrowed on the doctor. "Yeah, what of it?"

"You nursed it back to health back to health."

"It got run over a few weeks later. So?"

"So you spent the next month crying about it."

"What is your point, Ritsuko?"

The doctor sighed. "My point is: shit happens. Don't get attached to something if you can't handle losing it. You can have a good future here. Don't let Shinji be the anchor that chokes you down."

The major clenched her fist. "Come in HQ, this Rescue One. We have dislodged the Entry Plug and are bringing it down now," a man said over the radio.

Ritsuko picked up the receiver. "Copy that Rescue One, prep an emergency transport. I'll be there in two minutes," she said. She put the radio down and stood up. "Think about what I said. Hopefully you'll avoid a court martial."

"I want a court martial," Gendo Ikari growled. He and Stacker were sitting in his office.

The Marshal tried to think of a time when the Director was angry. Nothing came to mind. He found Gendo's human like behavior rather amusing. His stiff face made sure that the thought would stay with him.

Stacker locked his fingers together and leaned forward. "You don't mean that, sir," he calmly said.

"Yes I do, Stacker. She tried to disrupt our operation. I will not tolerate such insubordination. If word of this gets to the wrong people, NERV could be subjected to _another_ investigation," Gendo coldly replied.

"Sir, I should remind you that Major Katsuragi is trained as a Field Operative. She is a spy, not a staff officer," Stacker pointed out.

"You are making excuses for her, again."

"No, sir. I am not."

Gendo's eyebrow rose up. "Explain."

"Say what you will of Major Katsuragi, she is a capable soldier. Getting rid of her will not only cost us a good woman, we'd also have to spend money and man hours to make sure she stays quiet," Stacker said. The Director leaned back in his chair a bit.

"How do you know we won't just eliminate her after we let her go?" Gendo countered. Stacker smirked.

"Because the Katsuragi name still carries a lot of wait. If she were to die in some tragic 'accident,' even our patrons wouldn't be able to save us from the worldwide backlash," he said.

"That's an awfully big assumption to hang your case on," Gendo retorted.

"True, but you aren't a gambler when it comes to politics. Give her another shot. I'll straighten her out," Stacker offered.

Gendo rubbed his temple. His brow crumpled. A scowl fell across his lips. "Fine. Once we are down to Yellow Alert, I'll make her Pilot Manager. That will free up Ritsuko for other tasks," he finally decided.

"Thank you sir," Stacker said. He relaxed in his chair.

"But this will be her last chance. If she does anything so much as test the line, both of you will be on the next flight to Beijing; and this stays under wraps until I give the all clear. Understood?"

"Of course sir."

"Good. Get back to Command for now."

Stacker stood up and walked back to the elevator. He enjoyed the silent trip down. The doors opened. A sly smile curled on his lips. "Dr. Akagi, nice to see you. Why aren't you out in the city?" he asked. The blonde doctor just nodded in greeting.

"We just got the Third Child's Entry Plug into the maintenance bay. No one's been able to get a reading from it. But we have him. I thought the Director would like to hear it personally," Ritsuko said.

"Yeah don't expect much. How's Misato?" Stacker asked.

"Hovering above a nervous breakdown."

"Typical. Well enjoy you're little scientist on scientist chat," Stacker said. He head off down the main corridor.

Ritsuko rolled her eyes and started the security procedures to enter the elevator. She patiently waited to reach the top.

The obsidian room always made her nervous. Her heart beat faster with each approaching step. Gendo was looking out the window. "If you are here to tell me that my son is safe, don't bother," the Director stated. Ritsuko felt her cheeks flush with embarrassment.

"Sorry, sir. I'll—I'll be on my way then," she said. Gendo silently turned around in his chair.

"You are not dismissed, Dr. Akagi."

The blonde stopped. She felt sweat form on her brow. "I want your latest report on Project Zero," Gendo requested. Ritsuko bit her lip.

"I'm sorry sir, but I am not prepared for that," she said.

"Let me rephrase the question: have you made any progress with the cellular separation?" Gendo asked. Ritsuko shook her head. Her head slunk down. Her eyes met her feet.

Gendo stood up and walked up to the young woman. He placed a firm hand onto her shoulder. "Not every scientific achievement has to come over night," he said.

"Sir we—we haven't produced anything meaningful since my…since I took over," Ritsuko lamented. Gendo nodded.

"Be patient and trust that Stacker can hold off the Nephilim, and one day Ritsuko, it will be you who changes the world."

_To Be Continued..._

* * *

A/N: Hello and thank you for reading Chapter II. First off, a big thanks to Dragonlord001 for my first review ever. Your contribution is greatly appreciated and I hope to see you again.

This was kind of a strange chapter to write. At the time this chapter was posted, _Evangelion 1 _was a completed rough draft. I got this chapter onto my computer to find it extremely short. It was basically a utilitarian bridge to move us into the second act. Well screw that, I want to try my hand at some character development!

Onto the story proper with again more standard EVA fair. Shinji get's his ass beaten by a giant monster, awakens hidden power, proceeds to win. Ritsuko and Misato oversee the clean up. But hey, Gendo has it out for the Major and why is the Marshal so attached to her? What is Project Zero? How will Ritsuko change the world?

Honestly, this will probably go down as one of _Project: Apocrypha_'s weaker chapters. Like that one episode from Season 1 of _Avatar: the Last Airbender_. You know, the one that has literally zero to do with the plot of the rest of the show.

Please leave a review, ask a question, or send me an idea.

Until next time, watch the skies traveler.


	3. Chapter 3

The following is a non-profit, fan work based off the respective works of Hideaki Anno and Guillermo del Toro

All rights belong to the original creators, Legend Pictures, LLC; and Gainax Company, Limited

The Bluefire Phoenix presents...

A Chapter of _Evangelion 1: Today is (not) Lost…_

Chapter III: Welcome to NERV

_"First the Security Council splits off from us. Then they remove five trillion dollars from the budget? The world is burning and they think it's okay to spill the water down a hole?"_

_-Soundbite from US Amb. Kelly Wright's address to the UN General Assembly, 14 September 2003_

Shinji woke gasping for air. His panting went on for nearly a minute. The clinical smell disinfectant filled his nose. A bit of light filtered through the blinds of a window. He finally controlled his breathing and gazed upon a ceiling he didn't recognize. A sigh escaped his lips. "I'm…alive?"

Stacker Pentecost looked crosser than usual. Major Misato Katsuragi was before him in full dress uniform. She stood at attention.

The marshal flipped through her file. He skimmed over each page and then placed it atop another pile.

"This is unacceptable, Major. Truly unacceptable," Stacker began He had reached the last of the papers in the file. "Insubordination, accosting the Director in the middle of a red alert, usurping the chain of command. What could you possibly, _possibly_ have to say for yourself?"

"I was doing what was in the interest of Pilot Ikari, sir."

"And you think this gives you the right to bypass me and the Director?"

"No sir, I was trying to point out that Pilot Ikari lacked the sufficient skills to execute the director's plan."

"Don't you think we knew that, Major?"

Misato caught herself. She gave her lip a bite. "You mean that was your plan! You thought you could—"

"Watch your tone Major," the Marshal growled.

"He's been out cold for three days. Was that part of your plan too?"

The Marshal relaxed just a little. "It bothers you that we used the boy, doesn't it?"

Misato grew silent.

"I know this isn't ideal. But we are not angels or saints. Shinji is the only one we have right now, and that is the terrible truth we have to live with," Stacker said. Gently locked his hands together and set them on his desk.

"But…there has to be someone else," Misato whispered.

"Major, I could have you court martialed and you are concerned about the boy?"

"Sorry sir."

"Working for NERV is important. But your actions the other day, dismal application, and your abhorrent lifestyle have led me to believe you think that this is a joke."

Misato hung her head. "It isn't, sir."

Stacker let out a sigh. "The Director wants your head, Misato. I was able to convince him otherwise."

The woman looked up. "You mean it? When do I go back to Japan?"

The Marshal looked off to the side for a moment. "You...you are not going back."

"What?"

"Now that the Third Child has been extracted, the presence of a NERV agent without cause would violate our charter and the Security Council would happily leave us high and dry for it."

"Then what are you going to do with me?"

"You have been assigned here as Pilot Manager."

Misato hand to use every microgram of will power she possessed. Purple veins popped out of her clenched fist. "I am a trained NERV agent, not some bureaucrat. This is a waste of my talents," she calmly said between deep breaths.

Stacker forced himself up to his feet. He locked eyes with Misato. "Enough Major. It is time to grow up and take responsibility."

Misato forced her eyes forward. "I am grown up!" She shouted.

"No, you are not. I know what went on in Japan. You spent every day like it was spring break. You have never taken anything seriously and so now I have to draw a line," Stacker countered. "Now you either accept this assignment or you leave. And if you leave you won't see Ritsuko or Shinji…or me ever again."

The last sentence sent a chill down Misato's spine. Her lips quivered into a frown. "Bu—I—no, you can't," she started to bubble out.

"What's it going to be, Misato?"

"I—I accept," she finally said. Stacker nodded in approval.

"This is your last chance. Think before you act and you'll be fine. Now go see Ritsuko. She'll inform you of your specific duties. Dismissed."

Stacker picked up a picture frame off his desk the moment Misato disappeared out the door. The frame held a photo of Stacker and a little girl at a beach. He was holding the girl in his arms. The girl's smile seemed too wide for her face.

Shinji was sitting up on his bed. His back was heavily bandaged up and he had stitching on the scratch on his face. Doctor Akagi was running some tests on him.

"You'll have a few scars, but no permanent injuries," she commented.

"Doctor what—what was that thing?" he quietly asked. The doctor paused in her work and turned to Shinji.

"I don't think I am one who should tell you that. You should ask Stacker or your father," she admitted. Shinji shook his head.

Ritsuko let out a sigh. "We call them Nephilim. Our best guess says that they are aliens that are crossing over from another dimension. We encountered something like them fourteen years ago. That's all I can tell you about that," she said.

"Aliens from ah—ah another dimension?"

The doctor nodded. "Sounds crazy, but the truth is we don't really know anything other than they seem programmed to destroy humanity. Pretty scary right?"

Shinji just sat there. Misato entered the room. A dejected look marred her face. "Oh, sorry for interrupting. I was told to report to you doctor," she said. Her voice was barely above a mumble. Ritsuko stood up and gave Shinji a passing pat on the head.

She walked by Misato who followed her out. "How did your talk go?" Ritsuko asked. The women started walking down the hall.

"Well I'm still here so there's that," Misato sighed.

The doctor and turned to the major. "I know we haven't been on good terms for a long time. But I'm glad you stayed," Ritsuko admitted. She looked down at her feet. A half smile crept onto Misato's face.

Do you mean that Rits?" Misato asked. The doctor nodded.

"You deserve all the time you can get with him. I never understood until—until a while ago," she admitted. Misato wrapped her friend in a hug.

Ritsuko patted Misato's back then broke the embrace. The blonde put on a sincere, amused smile. "Okay, okay. We can continue this later. Right now you need to get up to speed on what you're going to do since you're staying," she said.

The women walked to the barracks section of the headquarters. Crews were in the middle trading shifts or going to the mess hall. A couple of maintenance workers were repairing damage from the attack. Sparks flew off the blowtorch they used to remove the metal plating.

On duty soldiers saluted the women while the ones on break either gave a passing nodded or were too wrapped up in their conversations to notice. The atmosphere felt alive and relaxed. But Misato could see an edge of nervousness in their eyes.

Ritsuko stopped at an empty room. She used her ID to access the space. The door hissed open. They entered a decent sized common area.

Misato counted three doorways on the left and right side of the room with an actual door on the far side. The room felt rather cold and calculated. The feeling was amplified by the grey color scheme.

There were a few furnishings in the common room. Two green sofas and a coffee table occupied the giant center rug. Bookshelves occupied the far wall.

The Major spotted a chalkboard by the entrance. It was divided into twelve cells with tape. The left hand cells were nowhere near as long as the right most cells.

"This is the Icebox," Ritsuko said, "now that we have more than one pilot; we will have to move them in here." She opened the back door. "Back here is your office and bedroom. All bathrooms are across the hall."

Misato looked around the place. "You mean Ayanami is going to be here too?" She asked.

"Yes Misato, Ayanami too."

Those words caused Misato to shudder quite a bit. "Okay, so what do I do exactly?" She said after she regained control.

"Simple. Make sure they get to training on time, maintain a healthy diet, and keep an eye on their mental state," Ritsuko said.

"Sounds easy enough. I think I can do this!" Misato said.

"Is that enthusiasm I hear?" Ritsuko joked.

"I'm going to prove to him that I can do this. That I deserve my NERV badge," Misato declared.

"Well I hope you can keep up that attitude."

"Why?"

"Because the Marshal told me that if he catches even a whiff of alcohol, you're out."

Misato felt her eye twitch.

_What am I doing here?_ Shinji thought. Ritsuko and Misato had been gone for a while.

_Fighting alien monsters with a giant robot. I mean how did I even survive that?_ He continued to worriedly ponder. The battle started to come together in his mind.

The details started to come out. A headache from hell violently erupted inside his mind. Something else took shape in his mind's eye.

_Eye. Red. Madness._

_Tower. Fire. Watching._

"Ghaa! Ahh! Rhaa!" Shinji screamed. Alarms sounded around him. A nurse rushed to his side. Shinji saw her lips move but heard no words. He felt a prick in his arm followed by a return to darkness.

"Was it contamination?" He heard a familiar voice say through the fog in his mind.

"Something like that. But I can't tell," another voice answered.

The feeling in Shinji's right arm began to return. He clenched some cloth. Pain shot straight up his arm. A hand landed on his shoulder.

Shinji's eyes fluttered opened. Misato was hovering above him. "You all right?" She asked.

Shinji nodded. Misato smiled. "Good."

"Where am I?" Shinji asked. His voice was raspy and his throat burned.

"They call it the Icebox. It's our new home," Misato said. She helped Shinji up then got him a glass of water.

The boy took in his surroundings. He was now in a grey room that lacked a door. "Take it easy, kid," Misato said before she left.

On Shinji's nightstand were several manuals and guides. The sound of heavy boots stopped him before he could pick one up. In his door way was a tall, dark skinned man. His face was worn down and his hair was starting to grey.

"Hello Shinji," the man greeted. The boy felt the hair on the back of his neck stand up.

"Marshal," Shinji muttered.

Pentecost nodded. "Your recovery has gone well. That's good. I would have seen you sooner, but your father had the command staff on high alert until this morning," he said.

He walked a little closer. "Are you okay?" Pentecost asked.

Shinji turned his head away. "Why am I the only one who can pilot the EVA?"

"Isn't that the question that I've asked every morning since you arrived," Stacker mused. Shinji bit his lips. "The truth is I don't know."

Shinji looked up. "What?"

"All I know is that some people can be pilots, but most can't. What the rules are that determine that are above my pay grade. They just tell me who they are and I have to live with that fact," Stacker coldly admitted. He sat down next to Shinji.

"How many of us are there? Pilots I mean," Shinji asked.

Stacker pondered a moment. "Including you? Three. Two here at the GeoFront and one awaiting their unit to finish being manufactured at EuroCommand," the marshal said.

"Three? You're protecting the world with three pilots?" Shinji shouted. He felt his heart pound faster and faster. Stacker placed a firming hand on the boy's shoulder.

"Shinji I've known your father a long time. He knows what he's doing. In the meantime, read up and get ready," Stacker said. He stood up and started walking to the exit.

"Ready for what?" Shinji asked.

"Anything and everything, kid," Stacker said reached the door.

Gendo was sitting at a table in the center of a dark room. Large, strange machines dangled down from the ceiling. Each had a large red eye that was menacingly transfixed on the Director. Their grey, mechanical bodies creepily moved up and down on silent hydraulics. It gave the illusion that they were breathing.

An unnatural silence gripped the room. The Director hid his expression behind his locked hands. He carefully pulled a file out of a silver briefcase.

"As you can see, the Evangelion project has proven successful at fending off the Nephilim. Just as you predicted," Gendo said.

One of the machines, numbered six on the side of its "head" moved in closer to Gendo. "Yes but the cost of repairing Unit-01 is far greater than we originally anticipated. Even as large as our resource pool is, we do have our limits, Ikari," it spoke in a heavily synthesized voice. Gendo calmly noted.

"I know, but this is a war. We can't expect the optimal result will occur in every battle. In fact I would say this encounter went better than anyone could have hoped for," he replied.

"That brings us to the issue of Unit-01's designated pilot. You've chosen your own son for the job. It seems highly inappropriate to give such a weapon to your own child," another one, marked number four, pointed out.

Gendo carefully adjusted his coat. "As you gentlemen know we have a very small pool of pilots to select from. It is an unfortunate coincidence that one of our pilots happens to be my son. But the Marduke Report clearly states that he is a legitimate pilot candidate. And we used him to that end," he said.

"And what of the Katsuragi girl?" the one designated number eight asked. Gendo bobbed his head slightly.

"I have decided to add her to my staff," he finally said.

"Is that wise?" number six asked.

"The Major is loyal to Pentecost and Pentecost is loyal to me. She will not be a...problem for you," Gendo answered.

The machine members looked at each other then back to Gendo. The largest of them, marked number one, approached the Directo. "You are skating on thin ice, Ikari. We swore to safeguard humanity's future. Do not make us break that promise," the it warned.

The robots faded away and lights came on, revealing a simple white room. The only door hissed open. Pentecost strode in. "So did they fire you?" he asked.

Gendo let out a snickering, sarcastic laugh. "Who would replace me? You?" he coolly jested. He stood up and walked up to the Marshal.

"Thought never crossed my sir. What's the plan in the mean time?"

"Training. Every day. Shinji's going to sink or swim, and he'd damn well better make the Olympic team."

"Sir, he was just released from the hospital wing. Shouldn't we give him a few days to recover?" Stacker asked. Gendo morbidly shook his head.

"He's back on active duty as of now."

Stacker frowned. "He's still a kid, Gendo. Can't we just pretend that he's normal?"

"Shinji hasn't been 'normal' for fourteen years."

Shinji stared up at his new unfamiliar ceiling. His clock read 22:37. He should have been asleep. He should have been dreaming.

But every time he closed his eyes, he felt as if he were back in the cockpit. His body would start to ache and his head would become inflamed. He could hear the Nephilim roar. He could smell the smoke.

So he lay sprawled out atop his cot, eyes gazing into the nothingness above. His mind swirled with stats, tactics, and jargon from the books he was given. The restlessness was starting to eat at him as the clock continued to tick away.

The curtain that acted as his only source of privacy shifted a bit. Shinji looked up to see Misato standing in the doorway. She was wearing a short nightgown. The boy felt his cheeks redden as his eyes inadvertently moved up the woman's slender legs.

He embarrassingly turned away. "Sorry, my stuff hasn't arrived yet. I had to borrow this from Ritsuko," she said. "May I come in?"

Shinji shook his head. Misato frowned. "Well I just wanted to say that you were very brave the other day. I don't think I could have done it. Anyway you should get some sleep. I'll...see you tomorrow."

_To Be Continued..._

* * *

A/N: Hello and thank you for reading Chapter III. Just as a heads up, don't expect this kind of speed for every project. Most of this story is done already, so it's a matter of editing it, writing these notes, and publishing it to the site. We're approaching one hundred views in just two days. That's pretty exciting.

I actually really like writing this chapter. Not a lot going on, but plenty of relationship stuff. Misato and Stacker have there first real conversation. Yes I played the pronoun game with you at the end of it. But I'd like to think that you guys and girls are smart enough to put two and two together. Shinji learned what the Nephilm are. Got to love that quick and utterly disposable explanation from Ritsuko.

/|Aliens|\

(I was trying to do that thing Giorgio Tsoukalos does on _Ancient Aliens_, I don't think it worked)

Back to my reality. So yes, as far as we know the Nephilim are just another alien race seeking the destruction of humanity. Big surprise there. Misato and Ritsuko have a nice chat about Misato's new job, mixed with a couple of character moments. Inadvertently, I have really enjoyed writing these two. Stacker and Shinji discuss why Shinji is a pilot. And Gendo talks with the GLaDOS cosplay committee.

Oh and Shinji had an apocalyptic vision possibly caused by his budding PTSD. Just another day at the GeoFront.

What do you guys think? Leave a comment or a question for me. Maybe even review it!

Until next time, remember that Aperture Science does what they must, because they can


	4. Chapter 4

The following is a non-profit, fan work based off the respective works of Hideaki Anno and Guillermo del Toro

All rights belong to the original creators, Legend Pictures, LLC; and Gainax Company, Limited

The Bluefire Phoenix presents...

A Chapter of _Evangelion 1: Today is (not) Lost…_

Chapter IV: A Girl Named Rei Ayanami

_"Unit-00 is a prototype, designed for experimentation. What happened that day was a freak accident that fell well within acceptable deviations."_

_-From Dr. Gendo Ikari's Official Testimony for the "616 Report"_

Shinji splashed some water onto his face. The cold rush snapped the sleep right out of his eyes. He inspected his face in the mirror. The clock over the bathroom door read 4:58, 16 April 2016.

The boy carefully started to inspect himself in the mirror. Dark bags had started to form under his eyes. His hair shot off in every direction. He futilely tried to pat down the loose strands.

He accidently brushed over the upper half of the red, raw scar that ran from just outside of his right eye down to the edge of his lips. The trace contact sent a disproportionately sized jolt pain through his body. The boy tried his best to take it in stride.

The scar had recently become scaly to the touch, in the process shrinking the scar a bit. It now pulled the right side of his face into a permanent scowl.

A sigh escaped his lips. He picked up his tooth brush and applied some tooth paste to it. The dreary haze in his eyes started to lift as he scrubbed his mouth. He spit and rinsed his mouth out with a glass of water.

He walked out of the bathroom, into the hall way. His eyes shifted from side to side. He let out a relived breath and then went to the Icebox's door.

The boy bit his lip as it hissed open. The common room was empty save for the furnishings. He tiptoed back to his room and slipped on to his cot.

A blaring whistle destroyed the blissful moment. Shinji jumped up to his feet. Misato stood in his doorway wearing her uniform.

She had a devilishly playful grin on her face. The same one she had since Shinji started the NERV instituted morning routine. He didn't bother to resist her as she dragged him down the hall to the elevator bank.

They descended a few floors to what he heard a couple of technician's call the Lair. Shinji found the name somewhat fitting. The floor consisted of two containment chambers easily capable of fitting Unit-01, a central observation deck that oversaw both chambers, and a secondary observation deck for each of the chambers. They were linked by a narrow hallway system.

The first containment chamber was empty. Nobody ever wanted to go near it. The other chamber consisted of several racks. One of the racks held the limbless, metallic endoskeleton of an EVA.

Shinji always found the sight of it rather haunting. He did his best to ignore it while walking down the hallway to the changing room.

A white, rubbery outfit was waiting on the rack for him. He quickly stripped off his standard issue NERV clothing and put on the strange, space age looking outfit. It was called a Plug Suit, designed to keep his body in a perpetual state of calm.

Shinji hit the button on his wrist. The loose fitting suit became skin tight. He still hadn't gotten used to how restrictive the Plug Suit could get around the waist.

He tentatively walked to the Entry Plug station. A couple of technicians were running their final checks. They gave him the thumbs up and Shinji climbed in.

The Entry Plug was lowered into the awaiting EVA. LCL started to fill up the tiny chamber. Shinji didn't even notice. He felt the strange sensations of entering the drift.

A sense of peace and calm fell over him as he sat in the heart of the strange machine. Misato shouted something rather loudly over the comm system. Shinji groaned as he grabbed the controllers.

The view screen began to distort then formed Hong Kong prepared for battle. A giant, monstrous creature rose out of the bay. Shinji's weapon was a pulse rifle. He sighed as he began the drill.

It took an agonizing four hours for Misato to finally be pleased with his performance. The boy stumbled out of the Entry Plug and returned to his normal state of dress. He patiently waited for the elevator to rise up to the R-and-D level.

Dr. Akagi had taken it upon herself to be his personal tutor. So after each morning's training session, he reported to her office to get his schooling taken care of.

Shinji stepped out into the new hallway to find the doctor waiting for him. A wide, mischievous smile was draped over her face. That sent a chill down Shinji's spine.

"Good morning Shinji. We'll be forgoing today's lessons. I have something for you to do for me," Ritsuko said.

Shinji expectantly looked around. "What am I doing exactly?" He asked.

"The First Child is being taken off the inactive list today. As such she needs to be transferred to the Icebox. You are going to help her move," the doctor explained. "Here is where her current quarters are." Ritsuko handed him her paper

_The other pilot is off the inactive list. I—wait what!_ Panic suddenly flooded over the boy. "Hu—her, as in a girl? I have to live with a—a girl!" He stammered. Ritsuko looked rather faux-surprised at his response.

"You live with Major Katsuragi, don't you?"

"Yes, but she's—but—but she's—"

"She's what, Shinji?" a cross voice asked behind him. Shinji turned around to see Misato standing there, arms folded across her chest. Her expression wasn't at all amused.

"Misato! It's…well…ah you technically sleep in a different room. I can't—with a—girl," Shinji stammered.

"Sorry, kid, but NERV pilots have to be in synch with each other as well as their machines. But Misato will make sure you don't get too intimate," Ritsuko teased. The boy lit up red. Misato snorted down a laugh. "Have fun, Shinji. Major, if you'd come with me."

The women retreated into the doctor's office down the hall. "So what's up Rits? You've been keeping me of this whole damn floor since I arrived," Misato said as she sat down. The doctor took the chair behind her desk and leaned forward.

"I'd like to hear your assessment of our newest pilot," Ritsuko requested.

Misato raised an eyebrow. "I submitted my official diagnosis yesterday. It's on the record."

"Yes but I'd like your off the record diagnosis."

"Why? Is this a test?"

"No. Just a friend asking another friend about work."

"So how is he?" Ritsuko started.

Misato rolled her eyes. "Shinji is getting better, at least superficially. But I'm sure he's feeling increasingly isolated. Everybody's nice to him, but there's no one his age to talk to here. We need to send him to a school in the city."

"I've had this conversation with his father, and the answer is no," Ritsuko coldly stated. Misato clenched her fist.

"You cannot be serious. The kid is suffering and you won't do a damn thing to help? What kind of bull crap is that?" Misato growled.

"It's called following orders, Major. I'd love for him to go to school and make friends. He's a nice boy and probably deserves it. But he is also a valuable asset and a potential security leak waiting to happen. The Director doesn't want the Security Council breathing down our necks because the boy accidentally slipped something important to the general public," Ritsuko calmly stated.

The major visibly restrained herself. Ritsuko could see a purple vein bulge out of her forehead. "Very well," Misato filtered through her gritted teeth. "If that is the Director's decision I will respect it. But I still disagree with it."

"Your objection has been noted. Anything else?" Ritsuko asked. Misato aimlessly looked around the Spartan office. No pictures were hung on the wall, just a few diplomas from some very prestigious universities. Ritsuko's desk was a cluttered mess.

"Mmm, No. What about you?"

"Me?" Ritsuko looked a little confused about the question.

"Yeah. I mean you've been hiding something from me since I got her," Misato said. Ritsuko kept quiet, turning her gaze to the side. "Come on, I'm still your friend. I always have been your friend."

Ritsuko looked scared. Her body shook a little. "I…I never got to say goodbye to my mom, okay! I didn't even know she had cancer until my sister called me about the damn funeral!" Ritsuko resentfully bemoaned. She slammed her fist down on her desk. Tears started to roll down her cheeks.

Misato bit her lip. She reached out and grabbed the doctor's hand. Ritsuko finally broke down. The two sat there in the void of the doctor's sobs for a good minute.

"Thanks," Ritsuko said. She wiped her face. "You should—you should go make sure the pilots made it back, okay."

Shinji walked down the halls of an older section of the base. His eyes watched the numbers that identified each room. He tried to avoid the NERV personnel that were wandering the halls.

The ones that did see him almost immediately dropped whatever they were doing and walked over to him. They would ask how he was, how fighting in the Evangelion was, or just give him a high five. It was strange to be the center of attention.

He finally reached his destination after escaping a female admirer. Shinji wasn't quite sure if she was hitting on him.

The door was marked with a name. "Rei Ayanami? That's a pretty ominous name," Shinji quietly commented to himself. He hit the buzzer.

Half a minute past. He buzzed again.

He went in to buzz a third time. His hand slipped and he hit the open button. The door slid open. Shinji gulped.

"Uh hello? Ms. Ayanami? I'm—I'm coming in," Shinji said. He tentatively entered.

The room was empty. There were a few packed boxes near the door. Shinji crept further in.

He spotted a cot. There was a girl sleeping on it. Shinji reached out to wake her.

_Is she not wearing a shirt? _Shinji thought as he placed his hand on her bare shoulder. A familiar pain took over his mind. He collapsed to his knees, screaming in pain.

_Pits. Shadows. Rage._

The boy's agony stopped. He looked up to see the naked torso of the girl. She was gripping his hand.

Shinji averted his eyes. "I'm sorry Miss, I—I," he stammered.

The girl released his hand, stood up and walked over to a dresser where a uniform was folded. She started to dress herself.

"You had a Synch Ratio below fifty percent during your combat mission," she said. Goosebumps crawled up Shinji's skin as the cold, near-lifeless sound of her voice washed over him.

The pounding in Shinji's chest made him want to turn around and watch her. But he kept staring at an empty wall. "What?" he said under his breath.

"That scar on your face, it is from your battle, yes?"

"Yeah it is. How did you know about my Synch Ratio? The official report hasn't been submitted yet," Shinji pointed out.

"It hasn't healed properly. A superficial injury like that can only be sustained when a pilot's Synch Ratio is below fifty percent," Rei responded.

"What about when my unit's arm was torn off? My shoulder was torn but it healed right," Shinji added.

"You can turn around now," Rei said. Shinji stood up and looked at Rei. She wore a simple white NERV uniform. "A Synch Ratio measures how deep in the Drift you are. The less deep you are, the more data the onboard computer has to forcefully extract your brain. This is very traumatic to your subconscious and leaves your mind extremely fragile. So when the computer registers damage, your brain cannot cope with it and shuts down anything to do with that area. The LCL in the area crystallizes during necrosis, creating an improper scar."

Shinji blinked a couple of times. "Okay, but then why did my arm heal?"

"When the EVA's computer detects catastrophic damage, it briefly cuts your connection. You still feel the damage from the lingering effect, but the lack of a direct connection keeps the injury from becoming permanent," Rei explained.

"So the EVAs protect us?"

"Simply put, yes. Why are you here Pilot Ikari?" Rei asked.

Shinji quickly snapped back. "Oh right. Uh—I'm supposed to help you move to the Icebox."

Rei kept her face expressionless. She pointed to the boxes near the door. "You may take those to our quarters then," she said. Shinji nodded.

It was an eerie way back to the Icebox. Shinji noticed the girl had strange blue hair and red eyes! The NERV personnel gave them a wide berth. They watched Rei with weary eyes. No one even said hello or gave a passing nod.

Shinji didn't comment. _What's their problem?_ He wondered.

"Pilot Ikari, would you indulge a question from me?" Rei asked. Shinji paused for a moment, but nodded. "How do you feel when you're in the Drift? Where do you go?"

The boy had to think about it for a moment. "It's hard to describe. But if I had to put words to it, I'd say I go somewhere safe. Why?"

"I've never met someone else who has been in the Drift. I was just...curious," the girl admitted. The two continued in silence.

The day had been quiet for Marshal Pentecost. _Nothing but paperwork. Ah, the price of command._ He mused to himself.

His phone rang. He picked it up. "This is the Marshal," he said.

"What?"

"No, don't call security. I'll handle it myself."

"Then have Ritsuko take care of it if I'm not back in half an hour."

Pentecost hung up his phone and pulled a pistol out of his desk's drawer. He checked the ammo then hid it in his uniform. _Nobody should even know about that level, save for me, Gendo, and the Security Chief_. He thought to himself. He climbed down a maintenance ladder.

The officer descended further into the GeoFront's depths, past even the Lair and the lower storage units. It was a dark, dank journey.

He arrived at an isolated floor similar to the containment chambers above. He pulled out his pistol. There was a light on in an observation room. Pentecost climbed up the ladder and burst in.

Gendo was standing there. He was looking down at the only thing stored in the room. His frown was slightly less noticeable in the low light. Pentecost let out a relieved sigh.

"What the hell are you doing?" Pentecost asked.

"I wanted to see it."

"Well call me next time. You had me run all the way down here for nothing," Pentecost muttered.

"Sorry."

Pentecost walked over to the window. "Do you think we'll need it?" He asked.

"Such weapons were not meant to be wielded by mortals," Gendo commented. "Besides, I doubt it will even work with the EVAs."

"But do you think we'll need it?" Pentecost repeated.

"Pray that we won't," he quietly answered. The two men stared at the large object a little more.

Rei took only a minute to unpack her things. Misato arrived. Like the other NERV personnel, she didn't look pleased with the girl.

Shinji pulled the woman aside. "What's everybody's problem with Rei? I get that she's got the personality of a wooden board, but still," he asked.

Misato shook her head. She pulled out a scrap of paper and scribbled something on it. "Look this up when you have some time," she whispered before she left the room.

Shinji read what she wrote. _UN Investigation 13907. That can't be good._ He thought as he put the paper in his night stand's drawer.

"All pilots to stations. All pilots to stations," a computer said over the intercom.

The boy rushed out of the room. He dashed down the hall to the elevator. Rei held it open for him. They dropped a few floors to the Deployment Deck.

It was crowded with soldiers and mechanics working overtime on the multi-ton hardware that made up NERV's conventional forces. Several mag tracks ran through the deck, leading every direction.

Rei and Shinji ran to an awaiting train. Misato was waiting for them. The train rocked over to the Cage.

The pilots went to the changing room to put on their plug-suits. Shinji found the skintight uniform a bit awkward. But with it, he could easily maintain a sixty percent Synch Ratio.

They exited the changing room and entered the briefing room. Ritsuko and Misato were waiting for them. The doctor checked the stopwatch in her hand.

"Fifteen minutes. Not bad," Ritsuko mused aloud.

"Excuse me doctor, but was this a drill?" Shinji asked.

"Yes it was. Pretty good for your first run together," she commented. "The marshal wanted to say something to you but he's. Oh he's here."

Pentecost walked through a secondary door. He nodded to Ritsuko. "Alright. Since your arrival here, you two have undergone training for solo-ops. Well I'm here to tell you no more. It is highly likely that we will face a Nephilim that can wipe the floor against one Evangelion," he said. "So we are going to drill and drill and drill until you two can finish each other's sentences in your sleep."

And drill and drill and drill they did, all afternoon. Shinji felt like every bone in his body was on the verge of breaking. It took everything he had just to keep pace with Rei. Yet she easily beat him to the punch at everything.

Ritsuko and Stacker looked rather pleased at the results. "Impressive. She's almost back to her old level," the doctor commented.

"She is...something else," the Marshal added. He turned his attention to Shinji. The boy was laying down a suppressing fire so that Rei could advance on their current objective. It was a surprisingly professional maneuver. The two were already showing sides of synchronization.

The cold shower water felt like the sweetest godsend on Shinji's skin that night. He braced himself against the tile wall. His chest was still heaving from the workout.

Shinji began to slowly bring his body under control. His mind started to focus on Rei. _What is it about her? _He thought.

_Why does everybody avoid her?_ He continued as he rubbed down his tendered body with the generic soap product Misato gave him.

_Did she do something wrong? Is that report Misato gave me some sort of criminal investigation?_ Shinji started to ask himself. _Maybe I should read it just in—_

_No._ He scolded himself.

_She is my fellow pilot now. Her past is her past and I will respect it. If and when she wants to talk about it, she will tell me. _He decided.

Across the hall Rei sat on her cot with her uniform hung up on the rack by her doorway, leaving her only in her underwear. Her privacy was protected by a black curtain.

She was thoroughly examining her eerie pale skin. Her hands slowly ran over every inch of her body. Yet they were constantly drawn back to certain spots.

One was on her right forearm, near the elbow. Another was just below her left breast. A third spot was on the outside of her right calf.

Each time her hand reached a particular spot, the girl would wince. She would thoroughly rub it, scratch it, and stare at it.

Misato knocked on a panel outside then entered the room. Rei continued to trace over her body. "I just wanted to—what the hell are you doing?" the woman asked. She watched the strange girl preform the almost dance like movements.

"When I met Pilot Ikari today, I told him about his scar. I don't remember where I received that information or why I would have it, as I lack any scarring," Rei stated. The major shook her head.

"So why are you doing that?" she asked.

"Because, my body feels like I should have scars."

The Major rolled her eyes. "Arg. Whatever, just be ready for training tomorrow morning. Keep your weird crap to yourself and keep giving me results and we won't have a problem. Am I understood?" she growled.

"Yes major," Rei whispered. Misato stormed out of the room, leaving the girl alone to continue her strange performance well into the witching hour.

_To Be Continued..._

* * *

A/N: Hello and thank you for reading Chapter IV. Well we are almost done with the second act people. What an exciting time to be alive.

Okay while I liked writing Chapter III, I _really_ liked how this one came out. Starting off we have yet another quote from the oh so cleverly named "616 Report." After that the chapter proper begins. I was oh so tempted to do a bait-and-switch simulation scenario like at the start of _Wrath of Khan_. But you guys don't deserve that level of cliché writing. So I went with a more quiet opening by focusing on Shinji's daily routine. This also gave me a chance to bring up his new physical change.

But why give him such a visible scar? Well for one, I was never really sold on the way NGE presented Synch Ratios. So I added a more immediate, physical threat that blended nicely with the Drift. Two, I think its interesting that every morning Shinji has to see who he really is (a scared child) versus how everybody else wants to see him (the hardened bad ass pilot).

Past that, Misato and Ritsuko have a nice chat about Shinji's condition. Another thing that always kind of bugged me about NGE is the fact that NERV allowed the three most valuable assets they had out of their facility entirely unattended. So...uh, take that. Also Ritsuko has mommy issues.

After four chapters we finally meet Rei! And what a lovely meeting it was. Nothing says first impressions like screaming in pain like a pathetic loser, right Shinji? Anyway, after some heart felt exposition about the mechanics of the EVAs we have a little bit of a character conversation.

Sacker and Gendo discuss a secret weapon and then we speed run through an actual drill to get to some fan service, sort of. You know, if you're into shower musing, and a girl with a gap in her memory talking about what's wrong with her body. But it's not my place to judge.

So what did you think? Is Rei creepy enough for you? Will Sacker and Gendo stop playing the pronoun game? Where the hell are the other _Pacific Rim_ characters? Will I finally stop dancing around with all this character building crap and get the plot moving again? Give me a review and tell me the answers!

Until next time, I have been and always shall be your friend*

*Terms and conditions may apply


	5. Chapter 5

The following is a non-profit, fan work based off the respective works of Hideaki Anno and Guillermo del Toro

All rights belong to the original creators, Legend Pictures, LLC; and Gainax Company, Limited

The Bluefire Phoenix presents...

A Chapter of _Evangelion 1: Today is (not) Lost…_

Chapter V: Round 2

_"Gendo's finally transferred me to the GeoFront to start training the so-called First Child. I fear this time of peace is starting to wind down. So what's next?"_

_-From Pilot Marshal Pentecost's Personal Log, 11 May 2012_

Rei slowly walked into the barracks' main rec-room. It was eleven hundred hours and the only other people there were some off duty soldiers using the PlayStation 4. They were rambunctiously cheering and swearing as they played their game.

It was a surprisingly diverse group, consisting of an American woman, a couple of guys from India, and a man and woman from China. They laughed and jeered as the score changed from one side to the other.

If any of them noticed Rei, they didn't say anything. The girl went over to another television in the corner. She sat down on the couch in front of it. Her back and shoulders cried out in protest before they were soothed by the soft sofa.

Never once did her emotionless façade betray her pain. She focused on the news program that was playing on the television.

It was a piece on the Jaeger Project currently in discussion in the United Nations General Assembly. Rei heard about it a couple weeks ago, just two days after she met Third Child. The Jaeger Project had only been out in the public eye for a short while. But it had gained a lot of popularity in that time. Most people felt that it was the less secretive option to the Evangelion Project.

The girl had a suspicion that the Jaeger Program would quietly disappear in a few weeks. It was a "gut feeling," as Major Katsuragi would put it.

Rei felt little for her supervisor. Major Katsuragi had the same suspicious nature that all the other NERV personnel had. Dr. Akagi was one exception, though she seemed more interested in Rei's metrics. But the doctor provided Rei a mantra that had served the girl well.

The Marshal showed some concern. But he was a soldier at heart. Rei knew that if the situation called for it, he would cut her away without a second thought.

Only the Director had shown her any real affection. He always smiled at her, always asked her how she was doing. Sometimes they'd dine together. Those moments always stuck with her.

The only other person that gave her that kind of care was—

Shinji stumbled through the door main on rubbery legs. His hair was damp from a recent shower. They were dressed in a similar fashion; a grey shirt with the red NERV logo across the chest and loose fitting gym shorts.

The boy crashed face first onto the couch, next to Rei. He released a long moan in pain. "Hey Rei," he finally murmured through the cushion. Rei double checked the clock.

"Shouldn't you be in class?" she dryly asked. Shinji slowly flipped onto his back.

"Dr. Akagi just got back from New York. She gave me the day off," he said. Rei just nodded

The two watched the television for a moment. "How do you get your Synch Ratio so high?" Shinji asked.

Rei turned to him with her expression only showing a hint of confusion. "I fail to see your point. The difference between our end-of-operation SRs is point-oh-five," she mechanically recalled. Shinji shook his head.

"No not that. You get in the Entry Plug and you start with like an eighty percent ratio. I'm lucky to be at sixty-five percent," he clarified.

"I—"

Shinji looked up then put his finger on his lips. "Wait for it," he whispered.

A yellow strobe light went off in the room. A low siren looped over the speakers. "Yellow alert. Yellow alert. All personnel to stand-by stations," a computerized voice said via the intercom. The soldiers quietly turned off their game and quickly filed out of the room.

The boy let out a low moan. "Well there goes my day off," Shinji muttered. He stood up and offered Rei his hand. Rei looked at it and then up to Shinji's face. "I'm trying to help you get up."

"Oh," Rei responded. Her cheeks reddened a bit as she took his hand. Shinji gently began to pull the girl onto her feet. She felt no pain in Shinji's grasp.

Their eyes, filled with a certain innocence, locked as the young woman rose up. Time slowed down around them. The sound of the alarm faded away. The strobe light created dynamic shadows across their skin. Their heads grew closer and closer as Shinji drew his arm to his chest. Their quivering lips were mere centimeters apart.

"Hey you two; we have work to do!" Major Katsuragi shouted from the doorway. The children broke off. Shinji scurried out the door first. The Major stopped Rei before she could follow.

"Do I have to warn you about pilot fraternization?" Katsuragi menacingly asked.

"No, ma'am," Rei responded.

"Good," the Major said. She escorted Rei down the briefing room. The Marshal was waiting. The main screen behind him was occupied by a map of the Pacific Ocean. The Breach was marked near the center of the vast sea.

Rei took the seat next to Shinji. Major Katsuragi stood off to the side. Pentecost walked up to the screen and pointed to the Breach.

"Thirty minutes ago, we detected movement in the Breach. Ten minutes ago, a Nephilim emerged and is currently heading for Hawaii," Stacker began. He moved his hand over to the appropriate island chain. "In another ten minutes, we will activate the Siren Song. This will give us ten hours to mount a defense," Pentecost summarized.

Shinji looked nervous. Rei raised her hand. "Sir, what is the size of this Nephilim?" she asked.

"Our initial estimates put it at a third bigger than the one Shinji faced. We won't have more until our survey team catches up with it. Any more questions, Ayanami?"

"No, sir."

"Very well. We'll meet up in the Cage's Briefing Room in five hours to finalize our defensive strategy. Dismissed."

Pentecost walked up to Command and Control after the pilots left. Misato wasn't far behind him. "Marshal, could I have a word?" She asked before they entered the chamber.

"What is it, Major?" Pentecost said in his usual professional manner.

Misato stopped walking. Pentecost turned around to see the woman looking at her toes like a nervous schoolgirl.

"I just...I just wanted to—to thank you," she said.

"Thank me?"

"Yes sir. You've looked out for me all these years. You're still looking out for me, and I have never appreciated it. I'm sorry I've been such a burden," Misato said.

Stacker loosened his strict stature. He walked over to her and wrapped her in a hug. He could feel tears roll off of Misato's face.

"You've never been a burden, Misato. I made a promise to you, and I'll never break it," he said. He placed a gentle kiss on Misato's head. "Now we have to plan a defense."

The two entered the Director's post. Stacker brought up a virtual representation of the city. "While we are on the subject of forgiveness, do you think you've been too hard on Ayanami?" he asked. He started drawing up battle lines.

"She's just another soldier," Misato responded.

"True but showing her a little human kindness now and again couldn't hurt," Pentecost suggested. Misato looked over to the main display.

"I honestly don't think she _is_ human," Misato retorted.

"Then maybe you should at the very least start treating her like one."

Gendo Ikari overlooked the GeoFront from his office. It was rather surreal to see the NERV soldiers working against the serene green background.

_How many will it take?_ He pondered. The elevator to his office hissed open. He turned around. Rei stood in the doorway.

"Hello, Rei. What are you doing here?" he asked.

"We will deploy soon," she said. She stepped forward.

"Yes. This will be your first combat mission. Are you nervous?" Gendo asked.

"No, but I am concerned about Pilot Ikari. He's been in his room for the past hour," Rei said. "Perhaps you should speak with him?"

Gendo shook his head. "My words would mean nothing to him," he said. There was a strange, slightly bitter glimmer in his eyes. "But perhaps you, Rei, could help him."

Rei stood in silence for a moment. "As you wish," she said. She departed, leaving Gendo alone again.

_What if last time was a fluke?_

_What if I mess up?_

_What if something happens to Rei?_

Those thoughts had rattled around Shinji's head since he learned of the attack. He sat on his cot with his hands cupping his eyes.

The boy felt a gentle hand on his shoulder. He looked up. Rei was standing over him with her cold persona.

"This is what we've trained for, Pilot I—Shinji. We will win," she said.

"So what? You're a natural at this!" Shinji shouted.

"Where is this coming from, Shinji?"

"I'm—I'm scared," Shinji whispered.

"What?"

"I'm scared alright! I'm not like you. I can't just turn it off like you!"

The two sat in an awkward void filled only by Shinji's nervous gasps. "I'm sorry Rei. That was—that was out of line," he finally apologized. Rei sat down next to the boy.

"Do you still want to know how synchronize so well?" She calmly asked.

"I suppose so."

"It's because I carry nothing into the Drift. No feelings, no attachment," she admitted.

"That's um, interesting? How did you learn to do that?"

"Dr. Akagi taught me."

Red strobe lights went off. "Red Alert, Red Alert. Pilots to the Cage! All hands to battle stations!" The computer said over the intercom.

Shinji checked his watch. He frowned.

"What the hell? We should have like three hours!" He cried. Rei stood up.

"It doesn't matter. We have orders," she said. She walked out of the room.

"Prepare the city. Delta configuration. Deploy for ground assault," Stacker barked at the Command and Control staff. They quickly got to work. A weird silent static gripped the room as silence fell.

Out in the GeoFront, the sound of massive hydraulics echoed around the main chamber. The buildings above started to sink into the ground. They formed massive steel stalactites above the facility.

"Damn it," Stacker muttered.

"You made an assumption about the Nephilim. Now we are going in blind," Gendo said as he stepped onto the terrace. "What's its ETA?"

"One hour and closing fast," Misato said.

"Alright, deploy the EVAs. Standard load out," Gendo ordered.

Shinji and Rei rode the elevator up to the top of the Cage. They could see their EVAs ready and waiting. The crews were finishing up last minute jobs.

Rei's Unit-00 was a head shorter than Shinji's unit. Its single large eye glistened in the light. The machine was painted in yellow.

Its armor plating was recently welded on over its joints and other weak spots. Those additions added to the already boxy design of Unit-00. The control arrays on its shoulders looked freshly attached as well.

Shinji's Unit-01 was a sleek beast in comparison. Its fearsome horned head and demonic face plate screamed of battle readiness, its dexterous clawed hands ready to bear the weight of battle. Its armor was inlayed with the chassis, creating only a few sharp angles along the exterior.

"So what did Ritsuko say to you that gives you your ability?" Shinji asked.

"Memento Mori," Rei said.

The boy recognized the phrase. It was Latin. "Remember—to die?" He whispered.

The girl nodded. "Yes. Make peace with your mortality. Let go of worldly things and entering the Drift will be nothing," she said.

"I think I understand," Shinji responded. The elevator stopped and the two exited. Rei looked at her unit for a moment. "You once asked me where I went in the Drift. So can I ask you the same question?" the boy asked.

Rei turned her gaze to the ceiling. "I feel like I've forgotten something and the deeper I go, the more I get…lost," she quietly said. She walked away. Shinji swore he heard sorrow in her voice. He sighed.

_I'm sorry you feel that way. I'm also sorry that I don't think I'll be able to follow your advice Rei. I'm just not like you. _ He thought as he stepped into his Entry Plug.

"How are you Shinji?" Misato asked via the comm-link.

"Terrified," Shinji admitted.

"It's okay. We've trained for this and we have Rei now. Say what you will of her she is...a damn good pilot," Misato said.

"Right," Shinji said. His unit was brought to a launch tube.

"Shinji, Rei, this is the Marshal. We don't know what exactly we're dealing with. So for the time being, your orders are to keep it occupied at a distance until we have a strategy. No heroics, am I clear?" Pentecost asked.

"Yes, sir," the two said in unison.

"Good to hear."

Shinji felt the familiar pang of entering the Drift. The pain, the warmth all meshed together. "Unit-01 ready for launch!" He heard over the strange bliss.

Reality returned with the sound of the Eva's safety locks disengaging. Shinji reached out and grabbed a rifle that sprang up from its case near his feet. Fear had been pushed back by instinct and training.

_Maybe they're right. I am ready for this. We're ready for this. I didn't need to be scared earlier._ Shinji thought.

Night had fallen over the city. A thin rain was falling.

Yet something else was in the air. A massive, ugly roar from near the shore line attracted his attention. He sprinted through the blocks of concrete and steel that now replaced most of Hong Kong's skyline.

He and Rei arrived at the beach just in time to see a massive creature emerge from the water. Shinji felt his heart stop.

The Nephilim towered over him by a good ten meters. Its shark-like head extruded hundreds of jagged teeth. A huge dorsal fin extruded from its back. Long thick arms dragged heavy hands along the ground as powerful legs propelled the beast forward.

The creature let loose a monstrous, window shattering roar. All of Shinji's fear rushed back in. He couldn't feel his body what's so ever.

The beast raised an arm up and Shinji found himself flying backwards.

_To Be Continued..._

* * *

A/N: Hello and thank you for reading Chapter V. Well the action is almost back, yay! And we are near the final chapter, boo!

Oh and to avoid flames, events occurring in the 2001-2003 A.D. range ruined the launch of the original Xbox, so Microsoft gave up on the franchise. The PlayStation 2 was safe because of an earlier release date and an established fanbase from the PS1. Yes I _am_ that petty, but I will miss the 360.

More of the same overall though. Shinji and Rei have a moment ruined by an almost jealous sounding Misato. That was fun, writing that melodramatic fluff knowing that a harbinger of destruction is on its way to kill them.

So if you are thinking and/or worried that Misato is replacing Mako Mori, well don't worry. There are some parallels that can be inferred from what we know of this Misato's back story and the canonical Mako's, yes. But Mako has her place here too. Sort of.

I see fun times ahead for our heroes. What about you? Where are they heading? Anything that you think is missing or that you'd like to see? Tell me in a review or send me a message. I love hearing from my readers.

Until next time, the Kinect is watching you sleep


	6. Chapter 6

The following is a non-profit, fan work based off the respective works of Hideaki Anno and Guillermo del Toro

All rights belong to the original creators, Legend Pictures, LLC; and Gainax Company, Limited

The Bluefire Phoenix presents...

A Chapter of _Evangelion 1: Today is (not) Lost…_

Chapter VI: The Fire of Heaven

_"Judgment Day is upon us my children. Heaven has opened and God shall greet us! Let us go to him and be reborn!"_

_-From Rev. Matthew Katsuragi's Antarctic Proclamation, 29 March 2002_

"—okay? Unit-01 report!" Misato shouted over a wave of static in his ear. Shinji opened up his eyes. His head was spinning in every direction.

The pilot found his back to be in tremendous pain. His EVA was lodged into one of the city's concrete barriers. He brought up his HUD. Hong Kong was burning and there was no sign of the Nephilim or Rei.

There was no serious damage at the moment. Shinji let out a sigh. Damn it. He angrily thought. I thought I could handle this but at the first sign of trouble I just froze up.

"This is Unit-01. I'm fine. Sorry I thought—"

"Don't beat yourself up Ikari," Marshal Pentecost interrupted, "I sent you in with insufficient data. Right now I need you to assist Unit-00. We have a plan but we need two EVAs for it to work."

An objective marker popped up on Shinji's HUD. He groaned a bit as he got out of the vertical crater. Rei was just over two kilometers away. The boy kicked it into overdrive.

He weaved his way through the fortress city. The scattered husks of tanks and helicopters and civilian cars littered the streets. Shinji could smell the smoke and death lacing the air. It mixed with the stench of blood in the entry plug.

His Synch Ratio was a high eighty-nine percent. The sound of gunfire echoed around him. Hold on Rei. Shinji pleaded.

The city blurred by. Shinji leapt over some rubble and brought his weapon to bear. The Nephilim was pursuing Rei's yellow unit.

Rei was retreating and firing, keeping the creature at a distance. She skillfully dodged an incoming strike and laid down a quick suppressing fire. The few bullets that slipped through bounced off its hide.

The creature lunged with its jaw. It found a mouth full of rubble instead.

"Alright, let's go!" Shinji shouted. He opened fire as charged.

Misato was wringing the railing on the command terrace. Two hours had passed since the Nephilim had made landfall. Two hours and nothing had stopped it. None of their plans had worked.

Now it was clawing into the GeoFront. Rei and Shinji had been reduced to trying to distract it. That wasn't going well either.

Panic was boiling over in Command and Control. Ritsuko was quickly typing into her laptop. The room rumbled. The Director and the Marshal were having a silent but heated conversation. Misato walked up to Ritsuko.

"So I hate to ask but—uh what are our odds on, say a scale from one to screwed?" Misato asked.

"Cluster fucked," Ritsuko bluntly said without a moment's hesitation. Misato rolled her eyes.

"Wow you are just a pillar of optimism," the major sarcastically retorted.

"What would have me say? The thing's hide is like the unholy love child of Mithril _and_ Adamantium grafted onto freaking _Superman_. Plus it has an AT Field. Even if it didn't have reach on us, we'd be hard pressed to hit its core because the damn thing is on top of its head."

"So we can try so—oh my god, Rei!" Misato shouted. She stared at the screen, petrified in horror.

The Nephilim finally gave into the pilots' incessant peppering of bullets. Now it had Rei cornered in a concrete outcropping.

"Major, get Shinji on the line and keep him from doing something stupid," the director ordered.

"Yeah, sure just keep him from talking to it. Easy enough," Misato said. She placed her headset on.

Gendo turned to Pentecost. "Now see to it," he quietly ordered. The Marshal nodded and went to a phone.

_Oh, man. I have to save her! _Shinji thought. He reloaded his rifle. _I just need an opening and I can_—

"Shinji, I need you to stay calm and not do anything," Misato calmly said.

"Not do anything? Rei's in danger and you'll have me do nothing?" Shinji growled.

"Please Shinji, your father has a plan!" Misato pleaded.

The Nephilim grabbed Rei and started crushing her. Shinji heard her screams. "Yes because that's worked out so well thus far," he sarcastically spat.

"Now is not the time for an attitude, Shinji," his father coldly growled. The boy felt a rush of cold run down his spine. "Now get to drop point Charlie-Two."

"I won't leave Rei!"

"You've been given an order, Pilot Ikari. You must follow it out," The Marshal reminded.

"This is our last chance to save her. Just do it," Gendo added.

Shinji let out a low growled. He started towards the drop point. _I swear father, if anything happens to her there will be no forgiveness._ He promised.

The boy arrived at the appropriate spot. "What now?" He asked.

"You're about to receive a prototype weapon," the Director said.

A cargo box arrived at the exit point and launched something into the air. Shinji reached out and grabbed it.

The boy examined his new weapon. He blinked a couple of times.

"A sword? This is your prototype weapon? A sword!" Shinji cried out.

"You'll need to get a Synch Ratio to one hundred percent in order to unlock its true power," the Director said.

Stacker leaned in. "Are you sure that will even work?" He whispered. Gendo shrugged.

Ritsuko walked over and slammed her hands down on the table. "Are you serious? We can't be sure that Unit-01 won't go berserk again and Unit-00 could sustain serious damage," she hissed.

"It is an acceptable risk," Gendo declared.

Shinji focused in the heart of his machine. _Memento Mori, that's what Rei told me._

_Remember to die_

_Be at peace_

_With yourself_

_And the world_

_Let it all go_

_Father_

"His Synch Ratio is rising!" A technician called.

_The Marshal_

"Ninety-one, ninety-two!"

_Dr. Akagi_

"Ninety-six, ninety-seven!"

_Misato_

"Come on Shinji!" Misato shouted.

_Rei_

_No not her. I can't leave her! I—I—_

"Grah! Ahh!" Shinji screamed.

Misato's eyes grew large in awe. The night sky was banished in radiant light. She was joined by most of the staff as well. The woman slumped to ground, cradling her legs.

Ritsuko began scribbling notes down.

Gendo just smirked. "You didn't think you'd see the Fire of Heaven again?" He asked Pentecost. The Marshal shook his head.

"I hope you know what you're doing. This could start another Antarctica Incident," he warned.

Rei could barely see what was happening behind the Nephilim. But she could feel something. "Sun Kissed," she whispered.

Inside Unit-01, Shinji felt lighter than air. Power, no, unadulterated power pumped through his veins. His eyes were lit up with a red-orange glow around the irises.

He slowly walked towards the Nephilim. The creature turned around to see the commotion.

Shinj pointed sword at the beast. The blade was burning with an unnatural, yellow and orange flame. The air crackled around the fire.

The Nephilim let out a horrific roar and charged Shinji. The boy gripped the sword and swatted away the beasts AT Field. He followed up with swift slice across its chest. It stumbled back a bit, clutching the oozing wound.

"Rei, can you move?" Shinji asked.

The girl checked her status report. "Give me a minute," she requested.

"Done," Shinji responded. He stepped up and re-engaged the Nephilim. The boy started cutting the monster to shreds.

The flaming sword cut through the monster with the ease of a hot knife through butter. Only instead of resulting in a slice of slightly melted butter, Shinji left charred chunks monster flesh behind.

He felt himself lost in the carnage. Each swing of the sword felt as if his body were enjoying the finest climax.

The creature's arm was nearly hacked off. Globs of gooey blue blood rained down on the city streets. The wounds were quickly burned closed and quickly reopened to bleed again.

The ground crew's mood quickly dived into the horrified range as they watched Shinji mercilessly slice open the creature again and again. Its screams of anguish and suffering echoed around the city. Shinji refused to yield.

"You need to end this now!" Gendo ordered. All he heard was the frantic breaths of the boy. "That's an order, Shinji."

"It escaped! It must be punished!" Shinji growled. There was a strange resonance to his voice, as if someone else was speaking at the same time. The boy continued the onslaught.

"What the hell is going on?" Pentecost demanded.

"His Synch Ratio is starting to creep up. He's at one hundred and six percent and climbing!" A technician reported.

"Any sign of contamination?" The Marshal followed up.

Ritsuko started to nervously curl her right hand. "Not contamination per se, but there is something similar to what we saw when Shinji collapsed after his first battle," she reported.

"Very well," Gendo said. "Shinji, if you don't finish it, we are going to cut the power to your unit."

A creeping silence followed. The attack stopped. The Nephilim started to slowly limp away. Shinji stopped it by pinning the beast's tail to ground with his sword. It let out a bellowing sob of agony.

Command and Control waited patiently. Only Misato's quiet, random mumbles could be heard.

Rei watched from a monitor in the Cage. Mechanics were working overtime to get her back in the fight. The girl couldn't remove her eyes from the screen.

She stared at Shinji's sword. There was a pang of envy in her eyes. Her hand inadvertently reached out and tried to grab the sword.

Shinji closed his eyes. His body was alight with energy. Static poured from his fingertips.

A voice, a beautiful voice told him that he needed to punish the abomination before him. The EVA agreed, pulling Shinji deeper into the Drift. Shinji tried to resist. But every time he raised an objection he was shot down.

His father's ultimatum silenced the other voices. He had to exert control now!

His eyes opened. He quickly pulled out the sword and grabbed the Nephilim by the throat.

He cast the creature to the ground and liquidity jabbed the blade through the red orb embedded in its skull.

The Nephilim was engulfed in purifying flames. Nothing remained but ashes.

Power left Unit-01 before the charred leftovers had even cooled a degree. Shinji found himself once again in the embrace of darkness.

A repetitive beep woke the boy up. He found himself once again in a hospital room. A sense of relief washed over him.

His greeting committee was less pleased with the recovery. He saw several guards aiming their rifles at him. His father was there and stoically watched the boy.

Gendo raised a digital recorder. His thumb gently hit the play button.

A horrible, maddening noise screech roared out of the tiny machine. Shinji felt as if the very essence of his soul was being ripped apart. He cupped his ears. His body began to convulse, twitching in every direction.

He spent an agonizing minute under the auditory torture. Gendo just watched. His face betrayed no emotion as he stopped it.

Shinji gasped for air. "Father," he moaned.

His father slipped the recorder into his breast pocket. He turned around and motioned for the guards to leave. They filed out quickly.

Misato burst in after Gendo and the troops marched. She ran to his side and helped straightened him out.

"Are you alright?" she asked.

"What the hell was that?" he groaned.

"It was a way to determine if you were contaminated. I'm sorry. There was nothing I could do to stop them," she said.

Shinji turned away. He let out a sigh.

"My words must seem hollow to you. But you need to talk about what happened, okay Shinji?" She softly coaxed. The boy sighed.

"I don't know," Shinji muttered. He curled up a bit.

Gendo stormed down the hall. He didn't even acknowledge Pentecost as he past.

"Gendo! You didn't actually do it did you?" Stacker called out. The doctor stopped and nodded.

Stacker kept his face neutral. "I'm sorry," he said. "But you were right, the sword was too much."

The Director shook his head. "I panicked. I thought we didn't have a choice. We could have come up with a better solution," Gendo growled. He quietly stormed off.

The marshal continued onto the medical ward. Misato was leaving Shinji's room. She looked dejected. She locked eyes with the marshal.

"That wasn't a prototype weapon, was it?" She asked in a whisper. Stacker bit his lip.

"What makes you say that?" Stacker asked.

"I remember seeing something like that in Antarctica. What was that sword? Where did it really come from?" Misato countered.

Stacker hardened his face. "Don't dig deeper that you should, Misato," he warned.

"Did it kill my parents?" She pressed.

"Misato," the marshal growled. Misato walked past him with a quiet huff.

The Marshal looked at the door to the Third Child's room and sighed.

Ritsuko waited patiently for the elevator to reach the Director's office. His memo sounded urgent. She had been swamped the last two days cleaning up the city. _This had better be important._ She thought.

The doors finally parted and she strode in. Ikari was sitting behind his desk.

"What is it, Director?" Ritsuko asked. She continued her advance.

Gendo frowned. "I need you to go down to Project Zero and prepare a replacement," he coldly ordered. Ritsuko's eyebrow rose on its own.

"Our current model is fine," Ritsuko pointed out.

"Yes but after Shinji's…incident, I have some concerns. If I don't see improvement, we'll swap them out once the replacement is ready."

Rei sat on her cot; her legs curled up to her chest and locked between her arms. Her red eyes bore into the grey wall. Sweat beads formed on her forehead.

She wore loose fitting NERV attire. The outfit ruffled as she anxiously rocked herself.

Blue hair shot up in random strands. Fresh stress lines had formed under her eyes.

The girl's head occasionally twitched. Her breath was ragged.

She spent hours in that state. Her stomach growled and her throat ached. The protest wasn't enough to get her to budge.

Misato knocked on the door. The woman entered the room. She walked in front of Rei and sat down against the wall.

The two locked eyes. It was a strange, silent battle of wills.

"Why are you here?" Rei coldly asked.

"Because it's my job to monitor your mental health. So, let's talk," Misato offered. Rei looked away. "You can tell me anything Rei."

Rei eyed the woman with suspicion. Misato just politely smiled.

"I feel…conflicted," she admitted.

"Why do you say that?"

"It's Shinji. When I think of him, this feeling of pride comes over me," she said.

Misato nodded. "That's good. You should take pride in the accomplishments of your teammates."

Rei shook her head. "No, it's something deeper than that. I can't express it in any meaningful way," she expounded.

"Okay, so where is the conflict you mentioned coming from?"

The girl loosened up her posture. She turned her gaze to the ceiling light. A deep breath exited her chest.

"When I saw him with...the sword, I felt envious," Rei admitted.

Misato's eyebrow cocked up. "Why do you think that is?" she asked. Rei shook her head.

"I don't know and it scares me," she admitted.

"Talk to Shinji," Misato asked. She stood up.

"What?"

"Talk to Shinji," she repeated.

"I—why can't I keep talking to you?" Rei pleaded. Misato shook her head.

"Because talking to me will only take you so far. If you want to solve your problem, take it up with Shinji," Misato said. She started to walk out.

"Wait," Rei requested. Misato stopped with her back to the girl. "Why do you hate me?"

The woman's shoulders slouched. She let out a sigh. "I don't hate you. I just know what the 616 Report says, and I've seen the footage. I'm not sure which one I believe," she said. Misato left the room.

Shinji was sprawled out on his hospital bed. His eyes were closed. The lights were off. The hum of an air conditioning unit was the only sound. The effects of that godawful sound were starting to wear off.

His hand involuntarily curled open and closed. He could still feel the sword in his hands. Its shadow felt as real as it had in the battle.

Someone opened the door and he heard loose clothing ruffle. He opened his eyes slightly. A smile curled onto his lips. It looked a little off due to his scar.

"Hello Rei," he said.

"Pilot Ikari, I wish…to speak with you," the girl said. Shinji nodded and indicated for her to sit down on the chair at his bedside.

She sat down. "I want to know what it was like to hold the sword," she said.

Shinji pondered a long moment. "It was terrifying. My body was all powerful, but my mind wasn't my own. It was like I had to share it with other—other things," he mused. A pleasant silence filled the space. Rei looked at her hands.

"When I saw you with it, I felt like I knew what I was looking for. For the first time in my life, something made sense beyond piloting an EVA," she admitted.

Shinji nodded. He reached out and grabbed Rei's hand. The girl was a bit taken aback by the gesture. Her head slumped to hide her reddened cheeks.

"Rei, I promise that I will help you find what you're looking for," he said.

"Wh—why?" Rei asked. Her body started to quiver.

"Because I'm done being scared. NERV can torture me, strip me of freedom, and turn me into their little toy soldier. But I'll be damned before I let them stop me from helping my friend."

"Friend? But didn't you see the report?" Rei asked. A wave of confusion washed over her. Shinji shook his head. "But why not? Everybody reads the report."

"Because I don't care about the girl in the report, I only care about the girl I know now," Shinji said.

"So we are…friends?"

"Until the very end."

The two could feel something between them. A beating heart seemed to grow between their clasped hands.

Outside the door, Ritsuko Akagi frowned. She slowly walked away.

Beyond the confines of the GeoFront. Away from the city of Hong Kong. Across the vast Pacific Ocean. Down at the deepest depths of the sea, a hellish purple and red portal slowly swirled around.

No life survived at the foot of the gate. The bodies of the tiny organisms that once thrived in the abyss piled up.

The portal led to some dark netherworld. The air was thick and alien. A vast, desolate plain of black stretched beyond the horizon save for a few distant, jagged mountain ranges. The sky was a deep purple filled with malicious, rumbling black clouds. A haunting roar echoed around the realm.

Deeper still in the strange world was an isolated valley in the middle of the largest mountain range. A silver casket lay in the middle of the barren basin. Rocks and boulders floated about.

A robotic probe hovered through the air. It stopped by the casket. The lid of the coffin began to slide off.

The probe stopped and waited as a naked boy emerged from the casket. The boy took in a deep breath. He examined his slender hands; a tinge of curiosity glazed his red eyes. Damp, silver hair draped down his face.

"Did you succeed?" the boy asked.

"Yes my lord. The fools were too caught up in the distraction to notice," the probe responded.

"Good. Have them begin work immediately," the boy said.

"By your command. But there is something concerning we discovered," the probe hesitantly stated.

"Well, spit it out," the boy disinteresting ordered.

"Ikari somehow recovered Uriel's Sword without our knowledge and has figured out how to use it."

The boy's left hand reflexively clenched and started to slightly twitch. He looked up at the purple sky. A frown curled onto his face. "Even now you still cast a shadow over me?" he angrily whispered.

"Shall I have the sword seized?" the probe asked.

"No, I will destroy the last remnants of Uriel…personally."

_End Part 1_

* * *

A/N: Alright kick the Aranda and roll credits, 'cause that's a wrap people!

_And if you ever feel ashamed, _  
_Like you're the one to blame_  
_And the weight of all the world _  
_Is on your shoulders crushing you. _  
_When the walls are closing in_  
_You gotta fight it from within _  
_Will you rise above the pain _  
_Or will you simply come undone?_  
_Will you rise above the pain or come undone?_

(From the song "Undone" by Aranda, all rights belong to them and their label company)

Yes we're done, finally. But man, lot's of stuff to talk about. Where the hell did NERV get a giant _flaming _sword that can change night to day? And why does Rei recognize it? What happened in Antarctica that's so damn important? Why did I just now introduce the main antagonist ? More importantly, do I actually plan to answer any of these questions?

Well, eventually I will. For now leave a review and tell me your favorite part of this story.

So let's talk about _Evangelion 2: Blood is (not) Thicker_. For one, don't expect it to be done in one weekend. _Evangelion 1_ was in the works months before I decided to post it here. Two, expect the first chapter out by the end of the month.

What can you expect from _Blood_? Well their is the arrival of a certain loudmouth red head, a look at the history between the Marshal and the Major, and sunshine and lollipops for everyone!_  
_

Until next time, you left your mark but I'm still in the dark


End file.
